Showing : affycoretools • reset
0
votes
3
replies
357
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 10 months ago by 58k • written 10 months ago by • 0
0
votes
2
replies
259
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
11 months ago luca.piacentini • 0
4
votes
5
replies
330
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 19 months ago by 58k • written 19 months ago by ▴ 780
3
votes
5
replies
359
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 22 months ago by 58k • written 22 months ago by ▴ 40
1
vote
2
replies
415
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 2.3 years ago by 58k • written 2.3 years ago by ★ 3.0k
1
vote
5
replies
403
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 2.6 years ago by 58k • written 2.6 years ago by ▴ 780
0
votes
3
replies
899
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
2
votes
4
replies
583
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 3.7 years ago by 58k • written 3.7 years ago by ▴ 10
1
vote
3
replies
612
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 3.8 years ago by 58k • written 3.8 years ago by ▴ 60
2
votes
4
replies
1.3k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 4.1 years ago by 58k • written 4.1 years ago by ▴ 30
2
votes
3
replies
953
views
Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
pd.hta.2.0 hta2.0 affycoretools
updated 4.2 years ago by 58k • written 4.2 years ago by ▴ 20
5
votes
4
replies
1.9k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 4.6 years ago by 58k • written 4.6 years ago by ▴ 780
9
votes
6
replies
2.8k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 4.7 years ago by 58k • written 4.7 years ago by ▴ 780
0
votes
3
replies
887
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 4.8 years ago by 58k • written 4.8 years ago by ★ 2.0k
3
votes
5
replies
848
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 6.5 years ago by 58k • written 6.5 years ago by ★ 2.0k
0
votes
4
replies
2.1k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 7.4 years ago by 34k • written 7.4 years ago by ▴ 50
0
votes
3
replies
1.3k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 8.6 years ago by 58k • written 8.6 years ago by ★ 2.0k
0
votes
0
replies
931
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
8.6 years ago Fiona ▴ 70
0
votes
7
replies
934
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 10.4 years ago by 58k • written 10.4 years ago by ▴ 350
0
votes
1
reply
686
views
why kOverA function has 6
affycoretools affycoretools
updated 10.5 years ago by ▴ 20 • written 10.5 years ago by ★ 2.0k
0
votes
0
replies
718
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
10.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
655
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 10.7 years ago by 58k • written 10.7 years ago by ★ 1.5k
0
votes
3
replies
1.0k
views
Help in installing affycoretools
affycoretools affycoretools
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 350
0
votes
0
replies
741
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
12.3 years ago James W. MacDonald 58k
0
votes
4
replies
3.0k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
13.0 years ago Celine Carret ▴ 220
0
votes
0
replies
679
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
13.1 years ago James W. MacDonald 58k
0
votes
2
replies
1.2k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 13.1 years ago by 58k • written 13.1 years ago by ▴ 80
0
votes
0
replies
710
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
13.1 years ago rgentleman ★ 5.5k
0
votes
3
replies
932
views
affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 13.4 years ago by 58k • written 13.4 years ago by ▴ 160
0
votes
1
reply
708
views
affycoretools question
GO limma affycoretools GO limma affycoretools
updated 13.4 years ago by 58k • written 13.4 years ago by ▴ 160
0
votes
10
replies
872
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 14.1 years ago by ★ 2.2k • written 14.1 years ago by ★ 7.4k
0
votes
3
replies
735
views
intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 14.5 years ago by 58k • written 14.5 years ago by ★ 2.2k
0
votes
3
replies
1.2k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 14.6 years ago by 58k • written 14.6 years ago by ★ 2.2k
0
votes
2
replies
836
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO Survival Biobase genefilter affy limma RBGL GOstats Category affyio affycoretools GO
14.7 years ago Mark W Kimpel ▴ 830
0
votes
1
reply
507
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 14.7 years ago by 58k • written 14.7 years ago by ▴ 830
0
votes
5
replies
909
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 15.0 years ago by ★ 7.4k • written 15.0 years ago by ▴ 890
0
votes
0
replies
625
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
15.0 years ago Kimpel, Mark W ▴ 890
0
votes
3
replies
2.8k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 15.0 years ago by 58k • written 15.0 years ago by ▴ 320
0
votes
0
replies
642
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
15.0 years ago James W. MacDonald 58k
0
votes
2
replies
780
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
15.4 years ago Kimpel, Mark W ▴ 890
0
votes
1
reply
465
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 15.5 years ago by 58k • written 15.5 years ago by ▴ 890
0
votes
6
replies
885
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 15.7 years ago by 58k • written 15.7 years ago by ▴ 20
0
votes
2
replies
664
views
justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
15.7 years ago Kimpel, Mark W ▴ 890
43 results • Page 1 of 1
Recent ...
Replies
Comment: Ensuring reproducibility in BiocParallel SingleCellExperiment workflows by Martin Morgan 25k
The lack of reproducibility has been true in the past, but I believe under the (just released) BiocParallel 1.28.0 setting `RNGseed = ` wil…
Comment: How to add pseudocount to DESeq2 dds object by Michael Love 34k
Yeah, what I meant to say was, if you have a sample that gives a 0 for a gene that nearly all other samples give a high count, does this sa…
Comment: How to add pseudocount to DESeq2 dds object by Stanley • 0
I looked at the genes with 0 counts in some samples and higher counts in others and there seems to be a pattern driven by sequencing run. …
Comment: Problem select / ensembl package by James W. MacDonald 58k
For example ``` > select(EnsDb.Hsapiens.v75, head(keys(EnsDb.Hsapiens.v75)), "SYMBOL") Error in UseMethod("select") : no applicable met…
Answer: Problem select / ensembl package by James W. MacDonald 58k
Looks like `select` is being masked by the tidyverse. Try using the fully qualified name `ensembldb::select`
Votes
DEXSeq throws a warning - rank-deficient matrix
C: DEXSeq throws a warning - rank-deficient matrix
Answer: preprocessReads: Can't remove more than 17 nucleotides
ensembldb support for Ensembl's transcript_name column
Answer: preprocessReads: Can't remove more than 17 nucleotides
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